The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

PLoS Genet. 2016 Nov 3;12(11):e1006421. doi: 10.1371/journal.pgen.1006421. eCollection 2016 Nov.


Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs). Many studies have found a large proportion of quantitative trait variation can be attributed to the additive genetic variance (VA), providing the basis for claims that non-additive gene actions are unimportant. In this study, we show that arbitrarily defined parameterizations of genetic effects seemingly consistent with non-additive gene actions can also capture the majority of genetic variation. This reveals a logical flaw in using the relative magnitudes of variance components to indicate the relative importance of additive and non-additive gene actions. We discuss the implications and propose that variance component analyses should not be used to infer the genetic architecture of quantitative traits.

MeSH terms

  • Analysis of Variance*
  • Chromosome Mapping
  • Genetic Variation
  • Phenotype
  • Polymorphism, Genetic
  • Quantitative Trait Loci / genetics*
  • Quantitative Trait, Heritable*